I'm getting the same "choppy scrolling" in Safari too. I'm using a 2010 13inch MBP, OSX 10.6.4, Safari 5, Extensions DISABLED, and YES all pages are downloaded completely.
As a comparison, I currently also have my 2007 iMac 2.4 C2D which scrolls any sort of web page in Safari 5 without an issue. This points to a definite problem with the 13inch MBP and NOT specific Safari 5 issue.
It leaves me wondering whether or not Apple are still having problems with the Drivers for the NVidia 320M. IIRC, I got my MBP with 10.6.3 on it and I'm pretty sure it was more snappy. If my memory serves correctly, Valve's Steam for Mac runs like ***** on 10.6.4 with Valve basically telling game users to avoid the .4 release untll driver issues have been resolved.